When you save an assembly as a multibody part, more internal data is saved. The additional data allows mates from the assembly to be retained in the multibody part. This is useful when you use the multibody part as a simplified representation of the assembly in a higher level layout assembly and then later need to make changes.
When you make changes to the subassembly and again save it as a multibody part, you can replace the old multibody part with the new one, without having to recreate the mates.
Only the active configuration of the assembly is saved in the multibody part. Configuration-specific properties from the active configuration, plus all custom properties, are saved in the multibody part, so you can use them in the BOM and annotations.